Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 57 of 187
Found at i:16796959 original size:9 final size:9
Alignment explanation
Indices: 16796941--16797005 Score: 53
Period size: 10 Copynumber: 7.0 Consensus size: 9
16796931 GTTCAGCCCG
*
16796941 AAGAAGAAA
1 AAGAAAAAA
16796950 AAG-AAAAA
1 AAGAAAAAA
* *
16796958 AAG-GAAAG
1 AAGAAAAAA
16796966 AAGAAAAAA
1 AAGAAAAAA
16796975 AAGGAAGAAAA
1 AA-GAA-AAAA
16796986 AAGAAGAAAA
1 AAGAA-AAAA
16796996 ATAGAAAAAA
1 A-AGAAAAAA
16797006 TATCACAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
8 13 0.28
9 8 0.17
10 16 0.34
11 10 0.21
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:16796971 original size:16 final size:16
Alignment explanation
Indices: 16796946--16797005 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
16796936 GCCCGAAGAA
16796946 GAAA-AAGAAAAAAAG
1 GAAAGAAGAAAAAAAG
16796961 GAAAGAAGAAAAAAAAG
1 GAAAGAAG-AAAAAAAG
*
16796978 G-AAGAA-AAAAGAA-
1 GAAAGAAGAAAAAAAG
*
16796991 GAAAAATAGAAAAAA
1 GAAAGA-AGAAAAAA
16797006 TATCACAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 1 0.03
14 9 0.24
15 5 0.14
16 13 0.35
17 9 0.24
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
GAAAGAAGAAAAAAAG
Found at i:16796981 original size:13 final size:12
Alignment explanation
Indices: 16796940--16796996 Score: 57
Period size: 11 Copynumber: 4.8 Consensus size: 12
16796930 GGTTCAGCCC
*
16796940 GAAGAAGAAAAA
1 GAAGAAAAAAAA
16796952 GAA-AAAAAGGAAA
1 GAAGAAAAA--AAA
16796965 GAAGAAAAAAAA
1 GAAGAAAAAAAA
16796977 G--GAAGAAAAAA
1 GAAGAA-AAAAAA
16796988 GAAGAAAAA
1 GAAGAAAAA
16796997 TAGAAAAAAT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
10 3 0.08
11 11 0.29
12 10 0.26
13 9 0.24
14 5 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAAAA
Found at i:16796987 original size:11 final size:10
Alignment explanation
Indices: 16796940--16797005 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 10
16796930 GGTTCAGCCC
*
16796940 GAAGAAGAAA
1 GAAGAAAAAA
16796950 -AAGAAAAAA
1 GAAGAAAAAA
* *
16796959 -AGGAAAGAA
1 GAAGAAAAAA
16796968 GAA-AAAAAA
1 GAAGAAAAAA
16796977 GGAAGAAAAAA
1 -GAAGAAAAAA
16796988 GAAGAAAAATA
1 GAAGAAAAA-A
16796999 GAA-AAAA
1 GAAGAAAA
16797006 TATCACAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
9 20 0.43
10 17 0.36
11 10 0.21
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (10 bp):
GAAGAAAAAA
Found at i:16797290 original size:18 final size:17
Alignment explanation
Indices: 16797267--16797305 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
16797257 CCCAATCTGT
16797267 AAAAAAAAAGAGAAAAAG
1 AAAAAAAAAGA-AAAAAG
16797285 AAAAAAAAAGAAAAAAG
1 AAAAAAAAAGAAAAAAG
16797302 AAAA
1 AAAA
16797306 GGCCCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAGAAAAAAG
Found at i:16797649 original size:20 final size:20
Alignment explanation
Indices: 16797626--16797664 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
16797616 GAAAATATTC
16797626 AAAAATTCTCGTGTTTTAAA
1 AAAAATTCTCGTGTTTTAAA
16797646 AAAAATTCTCGTGTTTTAA
1 AAAAATTCTCGTGTTTTAA
16797665 TAAGATCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
AAAAATTCTCGTGTTTTAAA
Found at i:16797826 original size:35 final size:35
Alignment explanation
Indices: 16797769--16797836 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
16797759 TACGGTATGT
16797769 TTTTTAAAAATTCCCGTATTTTCACAAAATTCCAA
1 TTTTTAAAAATTCCCGTATTTTCACAAAATTCCAA
* ** * *
16797804 TTTTTAAAATTTTTCGTGTTTTCAGAAAATTCC
1 TTTTTAAAAATTCCCGTATTTTCACAAAATTCC
16797837 CGTGTCGCCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (35 bp):
TTTTTAAAAATTCCCGTATTTTCACAAAATTCCAA
Found at i:16797928 original size:71 final size:72
Alignment explanation
Indices: 16797847--16797980 Score: 216
Period size: 71 Copynumber: 1.9 Consensus size: 72
16797837 CGTGTCGCCA
* *
16797847 AAAAAATTTTCGTGTTTTCTAAAAACTTCTGTGTTTCATAAATTTTCCTGTTCT-CAAAATTTCC
1 AAAAAATTTTCGTGTTTTCTAAAAACTTCCGTGTTTCAAAAATTTTCCTGTTCTCCAAAATTTCC
16797911 GATGATC
66 GATGATC
* * *
16797918 AAAAATTTTTCGTGTTTTCTAAAAACTTCCGTGTTTCAAAAATTTTCGTGTTTTCCAAAATTT
1 AAAAAATTTTCGTGTTTTCTAAAAACTTCCGTGTTTCAAAAATTTTCCTGTTCTCCAAAATTT
16797981 TCTTGATTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
71 49 0.86
72 8 0.14
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.45
Consensus pattern (72 bp):
AAAAAATTTTCGTGTTTTCTAAAAACTTCCGTGTTTCAAAAATTTTCCTGTTCTCCAAAATTTCC
GATGATC
Found at i:16797971 original size:36 final size:35
Alignment explanation
Indices: 16797809--16798111 Score: 236
Period size: 36 Copynumber: 8.4 Consensus size: 35
16797799 TCCAATTTTT
* * **
16797809 AAAATTTTTCGTGTTTTCAGAAAATTCCCGTGTCGCC
1 AAAAATTTTCGTGTTTTCA-AAAATTTCCGTGT-TTC
* *
16797846 AAAAAAATTTTCGTGTTTTCTAAAAACTTCTGTGTTTC
1 --AAAAATTTTCGTGTTTTC-AAAAATTTCCGTGTTTC
* * * *
16797884 ATAAATTTTCCTGTTCTC-AAAATTTCCGATG-ATC
1 AAAAATTTTCGTGTTTTCAAAAATTTCCG-TGTTTC
*
16797918 AAAAATTTTTCGTGTTTTCTAAAAACTTCCGTGTTTC
1 AAAAA-TTTTCGTGTTTTC-AAAAATTTCCGTGTTTC
* * *
16797955 AAAAATTTTCGTGTTTTCCAAAATTTTCTTGATTTC
1 AAAAATTTTCGTGTTTTCAAAAATTTCCGTG-TTTC
* * * * *
16797991 AACAATTCTCGTG-TTTCACAAATTTTCGCGTTTC
1 AAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTTC
***
16798025 AAAAAAAATCGTGTTTTCAAAAACTTTTCTCGTGTTTC
1 AAAAATTTTCGTGTTTTCAAAAA--TTTC-CGTGTTTC
* *
16798063 -AAAATTTTCGTGTTTTCAAAAATTTTCGTGTTTTT
1 AAAAATTTTCGTGTTTTCAAAAATTTCCGTG-TTTC
*
16798098 AAGAATTTTCGTGT
1 AAAAATTTTCGTGT
16798112 CTCTAAAATT
Statistics
Matches: 211, Mismatches: 40, Indels: 29
0.75 0.14 0.10
Matches are distributed among these distances:
34 31 0.15
35 49 0.23
36 57 0.27
37 38 0.18
38 8 0.04
39 27 0.13
40 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (35 bp):
AAAAATTTTCGTGTTTTCAAAAATTTCCGTGTTTC
Found at i:16798014 original size:107 final size:106
Alignment explanation
Indices: 16797809--16798095 Score: 279
Period size: 107 Copynumber: 2.7 Consensus size: 106
16797799 TCCAATTTTT
**
16797809 AAAATTTTTCGTGTTTTCAGAAAA-TTCCCGTGTCGCCAAAAAAATTTTCGTGTTTTCTAAAAA-
1 AAAATTTTTCGTGTTTTCA-AAAACTT-CCGTGT-TTC--AAAAATTTTCGTGTTTTC-AAAAAT
* *
16797872 CTTCTGTGTTTCATAAATTTTCCTGTTCTCAAAA-TTTC-CGATGATCA
60 TTTCTGTGTTTCATAAATTCTCCTGTTCTCAAAATTTTCGCG-T-ATCA
*
16797919 AAAATTTTTCGTGTTTTCTAAAAACTTCCGTGTTTCAAAAATTTTCGTGTTTTCCAAAATTTTCT
1 AAAATTTTTCGTGTTTTC-AAAAACTTCCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTTTCT
* *
16797984 -TGATTTCA-ACAATTCTCGTGTT-TCACAAATTTTCGCGTTTCA
65 GTG-TTTCATA-AATTCTCCTGTTCTCA-AAATTTTCGCGTATCA
***
16798026 AAAA-AAATCGTGTTTTCAAAAACTTTTCTCGTGTTTC-AAAATTTTCGTGTTTTCAAAAATTTT
1 AAAATTTTTCGTGTTTTCAAAAAC--TTC-CGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTTT
16798089 C-GTGTTT
63 CTGTGTTT
16798096 TTAAGAATTT
Statistics
Matches: 154, Mismatches: 11, Indels: 28
0.80 0.06 0.15
Matches are distributed among these distances:
105 6 0.04
106 23 0.15
107 78 0.51
108 13 0.08
109 3 0.02
110 28 0.18
111 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (106 bp):
AAAATTTTTCGTGTTTTCAAAAACTTCCGTGTTTCAAAAATTTTCGTGTTTTCAAAAATTTTCTG
TGTTTCATAAATTCTCCTGTTCTCAAAATTTTCGCGTATCA
Found at i:16801645 original size:2 final size:2
Alignment explanation
Indices: 16801638--16801667 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16801628 TTAGGTGTGA
16801638 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16801668 GTATGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16802110 original size:84 final size:86
Alignment explanation
Indices: 16801932--16802114 Score: 216
Period size: 84 Copynumber: 2.2 Consensus size: 86
16801922 TTGAGTATAA
* *
16801932 ATATGAAATTATACT-TATATATATATATATGTTAAATTCGAATATGTATGTGTATATAGGTATA
1 ATATGAAATTATA-TATATATATATATATATGTTAAATTCGAATATGTATATATATATAGGTATA
*
16801996 AGTTCTTGTTTCGAATATAAGT
65 AGATCTTGTTTCGAATATAAGT
* * ** * *
16802018 ATA-G-AATTATATATATGTATATATATTTGTTAGGTTCGAATATGTATATATCTATATGTATAA
1 ATATGAAATTATATATATATATATATATATGTTAAATTCGAATATGTATATATATATAGGTATAA
*
16802081 GATCTTGTATT-GAA-AT-GGT
66 GATCTTGT-TTCGAATATAAGT
16802100 ATATGAAATTATATA
1 ATATGAAATTATATA
16802115 GGTTATGTGG
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
82 5 0.06
83 4 0.05
84 68 0.82
85 3 0.04
86 3 0.04
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.44
Consensus pattern (86 bp):
ATATGAAATTATATATATATATATATATATGTTAAATTCGAATATGTATATATATATAGGTATAA
GATCTTGTTTCGAATATAAGT
Found at i:16802424 original size:41 final size:41
Alignment explanation
Indices: 16802360--16802628 Score: 434
Period size: 41 Copynumber: 6.6 Consensus size: 41
16802350 AGTAAGATGA
* * * *
16802360 TTCAGACTTTACATCTTGTAGGCTTGATGTCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
16802401 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
16802442 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
*
16802483 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
16802524 TTC-GAACTTTACGTCTAGCAGG-TTGATGCCGGTGAAATGT
1 TTCAG-ACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
* *
16802564 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
* *
16802605 TTCAGACTTTATGTCTAACAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
16802629 AATTGTTGGT
Statistics
Matches: 216, Mismatches: 9, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
40 37 0.17
41 179 0.83
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
Found at i:16802594 original size:122 final size:123
Alignment explanation
Indices: 16802360--16802628 Score: 434
Period size: 122 Copynumber: 2.2 Consensus size: 123
16802350 AGTAAGATGA
* * * * *
16802360 TTCAGACTTTACATCTTGTAGGCTTGATGTCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCT
*
16802425 TGATGCCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGT
66 TGATGCCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
16802483 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATATTTC-GAACTTTACGTCTAGCAGG-
1 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAG-ACTTTACGTCTAGCAGGC
*
16802546 TTGATGCCGGTGAAATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAAATAT
65 TTGATGCCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
* *
16802605 TTCAGACTTTATGTCTAACAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
16802629 AATTGTTGGT
Statistics
Matches: 136, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
122 80 0.59
123 56 0.41
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (123 bp):
TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATATTTCAGACTTTACGTCTAGCAGGCT
TGATGCCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAT
Found at i:16802666 original size:163 final size:164
Alignment explanation
Indices: 16802365--16802669 Score: 416
Period size: 163 Copynumber: 1.9 Consensus size: 164
16802355 GATGATTCAG
* * *
16802365 ACTTTACATCTTGTAGGCTTGATGTCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCTTGATG
1 ACTTTACATCTAGCAGGCTTGATGCCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCTTGATG
* * * ** *
16802430 CCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATGTTTCAGACTTTAC
66 CCGGTGAAATATTTCAGACTTTACGTCTAACAGGCTTAATGCCGGTGAAATGAATCAGACTTTAA
*
16802495 GTCTAGCAGGCTTGATGCCGGTGAAATATTTCGA
131 GCCTAGCAGGCTTGATGCCGGTGAAATATTTCGA
* *
16802529 ACTTTACGTCTAGCAGG-TTGATGCCGGTGAAATGTTTCAGACTTTATGTCTAGCAGGCTTGATG
1 ACTTTACATCTAGCAGGCTTGATGCCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCTTGATG
* ** * * **
16802593 CCGGTGAAATATTTCAGACTTTATGTCTAACAGGC-TAATTGTTGGTGTACTGAATCAGGTTTTA
66 CCGGTGAAATATTTCAGACTTTACGTCTAACAGGCTTAA-TGCCGGTGAAATGAATCAGACTTTA
16802657 AGCCTAGCAGGCT
130 AGCCTAGCAGGCT
16802670 AAGCACCGAT
Statistics
Matches: 121, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
162 2 0.02
163 105 0.87
164 14 0.12
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (164 bp):
ACTTTACATCTAGCAGGCTTGATGCCGGTGAAATGTTTCAGACTTTACGTCTAGCAGGCTTGATG
CCGGTGAAATATTTCAGACTTTACGTCTAACAGGCTTAATGCCGGTGAAATGAATCAGACTTTAA
GCCTAGCAGGCTTGATGCCGGTGAAATATTTCGA
Found at i:16803170 original size:71 final size:70
Alignment explanation
Indices: 16803094--16803250 Score: 208
Period size: 71 Copynumber: 2.2 Consensus size: 70
16803084 GATAAATACA
*
16803094 TATATACATTTGGTTATAATATTTGTTAAG-TATATGTATATATATGCATTCGGCTATTCATGTT
1 TATATACATTTGGTTATAATATCTGTTAAGATATATGTATATA-A-GCATTCGGCTATTCATGTT
16803158 CAAAGTG
64 CAAAGTG
*** *
16803165 TATATACATTTGGAGCTAATATCTGTTAAGCATATATGTATATAAGCATTCGGCTATTCATGTTT
1 TATATACATTTGGTTATAATATCTGTTAAG-ATATATGTATATAAGCATTCGGCTATTCATGTTC
*
16803230 ATAGTG
65 AAAGTG
* *
16803236 AATATACATTCGGTT
1 TATATACATTTGGTT
16803251 TTAAGAGTTG
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
71 61 0.82
72 1 0.01
73 12 0.16
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.43
Consensus pattern (70 bp):
TATATACATTTGGTTATAATATCTGTTAAGATATATGTATATAAGCATTCGGCTATTCATGTTCA
AAGTG
Found at i:16804326 original size:15 final size:16
Alignment explanation
Indices: 16804306--16804335 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16804296 GTTATGATAT
16804306 ATGAAA-TTTTTAAGA
1 ATGAAAGTTTTTAAGA
16804321 ATGAAAGTTTTTAAG
1 ATGAAAGTTTTTAAG
16804336 TTATAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (16 bp):
ATGAAAGTTTTTAAGA
Found at i:16804957 original size:60 final size:60
Alignment explanation
Indices: 16804859--16804996 Score: 204
Period size: 60 Copynumber: 2.3 Consensus size: 60
16804849 AGCAAGGCTA
* * * *
16804859 CAAACCCAACTCACAAGAACCTTGCGCGAGCTCATAAGGTAGGATCCCAGGTACAGCTCG
1 CAAAGCCAACTCACAAGAACCTTACGCGAGCTCATAAGGCAGGATCCCAGGCACAGCTCG
* * *
16804919 CAGAGCCAACTCACAAGAACCTTACGTGAGCTCATAAGGCAGGATCGCAGGCACAGCTCG
1 CAAAGCCAACTCACAAGAACCTTACGCGAGCTCATAAGGCAGGATCCCAGGCACAGCTCG
*
16804979 TAAAGCCAACTCACAAGA
1 CAAAGCCAACTCACAAGA
16804997 TAAGGTTACA
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 69 1.00
ACGTcount: A:0.34, C:0.30, G:0.22, T:0.14
Consensus pattern (60 bp):
CAAAGCCAACTCACAAGAACCTTACGCGAGCTCATAAGGCAGGATCCCAGGCACAGCTCG
Found at i:16811717 original size:35 final size:35
Alignment explanation
Indices: 16811671--16811739 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
16811661 AATAAAATAT
16811671 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTAG
1 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTAG
* *
16811706 ATTTTGTTTAACTTGACTTGCAAGGAATGTCTTA
1 ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTA
16811740 AAATTTGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.26, C:0.14, G:0.16, T:0.43
Consensus pattern (35 bp):
ATTTTGTTTAACTTGACTTGCAAGCAATCTCTTAG
Found at i:16817764 original size:26 final size:24
Alignment explanation
Indices: 16817733--16817788 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 24
16817723 ATTTTATGAT
*
16817733 TTTTATCTATTTTCCTTTATTGTTA
1 TTTTATCTATTTTACTTTATT-TTA
* *
16817758 TTATTATTTATTTTATTTTATTTTA
1 TT-TTATCTATTTTACTTTATTTTA
16817783 TTTTAT
1 TTTTAT
16817789 TTTACTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.15
25 7 0.26
26 16 0.59
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTATCTATTTTACTTTATTTTA
Found at i:16817768 original size:10 final size:10
Alignment explanation
Indices: 16817748--16817826 Score: 71
Period size: 10 Copynumber: 8.2 Consensus size: 10
16817738 TCTATTTTCC
16817748 TTTATTGTTAT
1 TTTATT-TTAT
16817759 TATTA-TTTAT
1 T-TTATTTTAT
16817769 TTTATTTTAT
1 TTTATTTTAT
16817779 TTTATTTTAT
1 TTTATTTTAT
*
16817789 TTTACTTTAT
1 TTTATTTTAT
*
16817799 GTTCA-TTTA-
1 -TTTATTTTAT
16817808 TTTA-TTTA-
1 TTTATTTTAT
16817816 TTTA-TTTAT
1 TTTATTTTAT
16817825 TT
1 TT
16817827 ATATGTCCAT
Statistics
Matches: 61, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
8 15 0.25
9 5 0.08
10 33 0.54
11 5 0.08
12 3 0.05
ACGTcount: A:0.22, C:0.03, G:0.03, T:0.73
Consensus pattern (10 bp):
TTTATTTTAT
Found at i:16817770 original size:4 final size:4
Alignment explanation
Indices: 16817761--16817874 Score: 86
Period size: 4 Copynumber: 26.5 Consensus size: 4
16817751 ATTGTTATTA
16817761 TTAT TTATT TTATT TTATT TTATT TTATT TTACT TTAT GTTCAT TTAT TTAT
1 TTAT TTA-T TTA-T TTA-T TTA-T TTA-T TTA-T TTAT -TT-AT TTAT TTAT
* * ** * *
16817813 TTAT TTAT TTAT TTAT ATGT CCAT TTTT TTAT GT-T TTAGT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT
16817861 TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TT
16817875 GTTGTTGTAT
Statistics
Matches: 93, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
3 2 0.02
4 53 0.57
5 36 0.39
6 2 0.02
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:16817787 original size:20 final size:19
Alignment explanation
Indices: 16817748--16817874 Score: 88
Period size: 20 Copynumber: 6.6 Consensus size: 19
16817738 TCTATTTTCC
16817748 TTTATTGTTATTATTATTTAT
1 TTTATT-TTATT-TTATTTAT
16817769 TTTATTTTATTTTATTTTAT
1 TTTATTTTATTTTA-TTTAT
* *
16817789 TTTACTTTATGTTCATTTA-
1 TTTATTTTAT-TTTATTTAT
16817808 TTTA-TTTA-TTTATTTAT
1 TTTATTTTATTTTATTTAT
**
16817825 TTATATGTCCATTTT-TTTATGT
1 TT-TAT-TTTATTTTATTTA--T
*
16817847 TTTAGTTTA-TTTATTTA-
1 TTTATTTTATTTTATTTAT
16817864 TTTA-TTTATTT
1 TTTATTTTATTT
16817875 GTTGTTGTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 26
0.72 0.07 0.21
Matches are distributed among these distances:
16 11 0.13
17 8 0.09
18 6 0.07
19 10 0.11
20 35 0.40
21 14 0.16
22 3 0.03
ACGTcount: A:0.21, C:0.03, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTATTTTATTTTATTTAT
Found at i:16817819 original size:52 final size:53
Alignment explanation
Indices: 16817761--16817874 Score: 137
Period size: 52 Copynumber: 2.2 Consensus size: 53
16817751 ATTGTTATTA
**
16817761 TTATTTATTTTATTT-TAT-TTTATTTTATTT-TACTTTATGTTCATTTATTTAT
1 TTATTTATTTTATTTATATGTCCATTTT-TTTATACTTTA-GTTCATTTATTTAT
** *
16817813 TTATTTA-TTTATTTATATGTCCATTTTTTTATGTTTTAGTTTATTTATTTAT
1 TTATTTATTTTATTTATATGTCCATTTTTTTATACTTTAGTTCATTTATTTAT
16817865 TTATTTATTT
1 TTATTTATTT
16817875 GTTGTTGTAT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
51 7 0.13
52 33 0.62
53 13 0.25
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.72
Consensus pattern (53 bp):
TTATTTATTTTATTTATATGTCCATTTTTTTATACTTTAGTTCATTTATTTAT
Found at i:16818190 original size:111 final size:109
Alignment explanation
Indices: 16817999--16818322 Score: 438
Period size: 108 Copynumber: 3.0 Consensus size: 109
16817989 CAAAAAAAAG
* * * * * * * *
16817999 AAAATTTTTCTAAATGAGGCAATATTTAGCTTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTGCT
** * *
16818064 GGGTGTCGATTTTTCTCGTTCAACCAAATTGCTTAATATTCTTTTAA
65 GGGTGTCGAGATTTCTCGTTCAACCAAATTGCTAAATA-TCCTTT-A
16818111 AAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTG
1 AAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTG
* *
16818176 GGTGTCGAGATTTCTCGTTCAACCAAATAGCTAAATATCCTTTC
66 GGTGTCGAGATTTCTCGTTCAACCAAATTGCTAAATATCCTTTA
*
16818220 AAAAA-TTACAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTG
1 AAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTG
* * *
16818284 GGTTTC--GATTTCTCGTTTAACCAAATTGCCAAATATCCT
66 GGTGTCGAGATTTCTCGTTCAACCAAATTGCTAAATATCCT
16818323 ATTGAATTTA
Statistics
Matches: 193, Mismatches: 19, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
106 30 0.16
108 63 0.33
109 5 0.03
110 5 0.03
111 51 0.26
112 39 0.20
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (109 bp):
AAAAATTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTG
GGTGTCGAGATTTCTCGTTCAACCAAATTGCTAAATATCCTTTA
Found at i:16821482 original size:22 final size:22
Alignment explanation
Indices: 16821454--16821497 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
16821444 ACAAAATACA
16821454 TATTCTCATATTCTACCTCACC
1 TATTCTCATATTCTACCTCACC
16821476 TATTCTCATATTCTACCTCACC
1 TATTCTCATATTCTACCTCACC
16821498 CAATTTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.36, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTCTCATATTCTACCTCACC
Found at i:16823657 original size:105 final size:104
Alignment explanation
Indices: 16823199--16823657 Score: 445
Period size: 105 Copynumber: 4.4 Consensus size: 104
16823189 CAGAGTGTTG
* * * * *
16823199 TATGTGACAACATCAGGCTCAATGCCTTGCTTTCTCATTCTGCCAAAAATATCTTCAGCTTCAGA
1 TATGTGACAACATTAGGCTTAATGCCTTGCTTTCTCATTATGCCAACAATAACTTCAGCTTCAGA
* * * * *
16823264 AACCATACTATTCTTGCAAAGTGAATCCATCAATATATTA
66 AACCATTC-CTTCTTGCAAAGCGAATCGATCAATATACTA
* * ** ** *
16823304 TACGTGATAACATTAGG-TTCAGCGCCTTGCTTTCTCATCGTGCCAACAATAAATTCAGCTTCAG
1 TATGTGACAACATTAGGCTT-AATGCCTTGCTTTCTCATTATGCCAACAATAACTTCAGCTTCAG
* * *
16823368 AAACCATACCATTCTTGCAAAGCGAATCTATCAATGTACTA
65 AAACCATTCC-TTCTTGCAAAGCGAATCGATCAATATACTA
** * * * * * * * *
16823409 TACATGACAACATTAGGTTTGATGCCTTGCTTTCTCATCACGTCAACAACAACTTCGGCTTTAGA
1 TATGTGACAACATTAGGCTTAATGCCTTGCTTTCTCATTATGCCAACAATAACTTCAGCTTCAGA
* * * * * *
16823474 AACC-TCCCCCATCTTGCAAAGAGTATCGATGAATATACCA
66 AACCAT--TCCTTCTTGCAAAGCGAATCGATCAATATACTA
* * * *
16823514 TATGTGACAACATTAGGCTTAATGCCTTGCTTTGTCATTATGCCAACAATATCTTCGGCTTTAGA
1 TATGTGACAACATTAGGCTTAATGCCTTGCTTTCTCATTATGCCAACAATAACTTCAGCTTCAGA
* * *
16823579 TATCATTCCTTGCTTGCAAAGCGCATCGATCAATATACTA
66 AACCATTCCTT-CTTGCAAAGCGAATCGATCAATATACTA
* *
16823619 TATGTGACGACATTAGGCTTAATGCCTTGCTTTATCATT
1 TATGTGACAACATTAGGCTTAATGCCTTGCTTTCTCATT
16823658 TCGAAGAAGA
Statistics
Matches: 291, Mismatches: 56, Indels: 14
0.81 0.16 0.04
Matches are distributed among these distances:
104 5 0.02
105 281 0.97
106 5 0.02
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (104 bp):
TATGTGACAACATTAGGCTTAATGCCTTGCTTTCTCATTATGCCAACAATAACTTCAGCTTCAGA
AACCATTCCTTCTTGCAAAGCGAATCGATCAATATACTA
Found at i:16826341 original size:20 final size:18
Alignment explanation
Indices: 16826326--16826375 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 18
16826316 TGAAAATATC
16826326 ATTAAAATTATAAAAAAT
1 ATTAAAATTATAAAAAAT
16826344 ATTAAAATTTTATAAAAAAT
1 ATTAAAA--TTATAAAAAAT
16826364 ATTAAAAATTAT
1 ATT-AAAATTAT
16826376 GTTTAAGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.24
19 4 0.14
20 14 0.48
21 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAAAATTATAAAAAAT
Found at i:16827755 original size:24 final size:24
Alignment explanation
Indices: 16827721--16827770 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
16827711 CAAAAAAAAG
*
16827721 AAAAAGCAGTCCAAAATCAATAGA
1 AAAAAGCAGTCCAAAAGCAATAGA
*
16827745 AAAAAGTAGTCCAAAAGCAATAGA
1 AAAAAGCAGTCCAAAAGCAATAGA
16827769 AA
1 AA
16827771 TATATGAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (24 bp):
AAAAAGCAGTCCAAAAGCAATAGA
Found at i:16830729 original size:5 final size:5
Alignment explanation
Indices: 16830719--16830744 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16830709 GGGTAAATAG
16830719 TTAAT TTAAT TTAAT TTAAT TTAAT T
1 TTAAT TTAAT TTAAT TTAAT TTAAT T
16830745 ATATTGTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:16834414 original size:441 final size:440
Alignment explanation
Indices: 16833588--16834471 Score: 1633
Period size: 441 Copynumber: 2.0 Consensus size: 440
16833578 AGAATTTGAT
*
16833588 GGAAATATGTTTCCTGAACCTAGGAGAGATAGAAGTGAACCTAGAGCTCCATCAAAAGGAAAATG
1 GGAAATATGTTTCCTGAACCTAGGAGAGATAGAAGTGAACCTAGAGCTCCATCAAAAGGAAAAGG
* *
16833653 CAATAAGCATACTTCTGTAGGCTCTTCATCTGGTAAAAGATCAAGCTCTAGTAACCTTGGGTATA
66 CAAGAAGCATACCTCTGTAGGCTCTTCATCTGGTAAAAGATCAAGCTCTAGTAACCTTGGGTATA
16833718 GTGATTCATCTACTAGCACTAAAGGTTTTTATCCATCAGAACAACCTTCATATTTTCAACCTTCA
131 GTGATTCATCTACTAGCACTAAAGGTTTTTATCCATCAGAACAACCTTCATATTTTCAACCTTCA
*
16833783 CATGGTTATCTACAACTATGTGGTTATTATCCACCATTTCCTAATTATGGTGTGCCATATCAGCT
196 CATGGTTATCCACAACTATGTGGTTATTATCCACCATTTCCTAATTATGGTGTGCCATATCAGCT
*
16833848 TCAAATGCATCCTCCACCACCAATGCATCACCCACCTCCACCTCTCATGTATCCTCCTCCTTAAA
261 TCAAATGCATCCTCCACCACCAATGCATCACCCACCTCCACCTCTCATGTATCCTCCTCCTCAAA
16833913 TATATCCTCCATGTCAATTATATGAAAACCAAAGTGAAAATGTTACTTTTTTCAATATATTTTCA
326 TATATCCTCCATGTCAATTATATGAAAACCAAAGTGAAAATGTTACTTTTTTCAATATATTTTCA
16833978 GATAAAGGCCAAGAGAATCAAGCCAAGAACACTCTCAAAATGAAGGTGAA
391 GATAAAGGCCAAGAGAATCAAGCCAAGAACACTCTCAAAATGAAGGTGAA
16834028 GGAAATATGTTTCCTGAACCTAGGAGAGATAGAAGTGAACCTAGAGCTCCATCAAAAGGAAAAAG
1 GGAAATATGTTTCCTGAACCTAGGAGAGATAGAAGTGAACCTAGAGCTCCATCAAAAGG-AAAAG
*
16834093 GCAAGAAGCATACCTCTGTAGGCTTTTCATCTGGTAAAAGATCAAGCTCTAGTAACCTTGGGTAT
65 GCAAGAAGCATACCTCTGTAGGCTCTTCATCTGGTAAAAGATCAAGCTCTAGTAACCTTGGGTAT
16834158 AGTGATTCATCTACTAGCACTAAAGGTTTTTATCCATCAGAACAACCTTCATATTTTCAACCTTC
130 AGTGATTCATCTACTAGCACTAAAGGTTTTTATCCATCAGAACAACCTTCATATTTTCAACCTTC
16834223 ACATGGTTATCCACAACTATGTGGTTATTATCCACCATTTCCTAATTATGGTGTGCCATATCAGC
195 ACATGGTTATCCACAACTATGTGGTTATTATCCACCATTTCCTAATTATGGTGTGCCATATCAGC
*
16834288 TTCAAATGCATCCTCCACCACCAATGCATTACCCACCTCCACCTCTCATGTATCCTCCTCCTCAA
260 TTCAAATGCATCCTCCACCACCAATGCATCACCCACCTCCACCTCTCATGTATCCTCCTCCTCAA
* * **
16834353 ATATATCTTCCATGTCAATTATATGAAAACCAAGGTGAAAATGTTACTTTTTTTTATATATTTTC
325 ATATATCCTCCATGTCAATTATATGAAAACCAAAGTGAAAATGTTACTTTTTTCAATATATTTTC
** *
16834418 AGATAAAGGCCAAGAGAATCAAGCCAAGAATGCTCTCAAAGTGAAGGTGAA
390 AGATAAAGGCCAAGAGAATCAAGCCAAGAACACTCTCAAAATGAAGGTGAA
16834469 GGA
1 GGA
16834472 TCTGATCCTC
Statistics
Matches: 429, Mismatches: 14, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
440 59 0.14
441 370 0.86
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (440 bp):
GGAAATATGTTTCCTGAACCTAGGAGAGATAGAAGTGAACCTAGAGCTCCATCAAAAGGAAAAGG
CAAGAAGCATACCTCTGTAGGCTCTTCATCTGGTAAAAGATCAAGCTCTAGTAACCTTGGGTATA
GTGATTCATCTACTAGCACTAAAGGTTTTTATCCATCAGAACAACCTTCATATTTTCAACCTTCA
CATGGTTATCCACAACTATGTGGTTATTATCCACCATTTCCTAATTATGGTGTGCCATATCAGCT
TCAAATGCATCCTCCACCACCAATGCATCACCCACCTCCACCTCTCATGTATCCTCCTCCTCAAA
TATATCCTCCATGTCAATTATATGAAAACCAAAGTGAAAATGTTACTTTTTTCAATATATTTTCA
GATAAAGGCCAAGAGAATCAAGCCAAGAACACTCTCAAAATGAAGGTGAA
Found at i:16839127 original size:76 final size:74
Alignment explanation
Indices: 16839035--16839255 Score: 309
Period size: 76 Copynumber: 2.9 Consensus size: 74
16839025 CTGGAGTATA
* * *
16839035 TTGAATATAAAAGGGGTTGCTAAGTGCTAATTTCCTGATTCATTGGTGGTTGCTAAGTGCTAATT
1 TTGAATAT-AAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTAATT
16839100 CCACCATATC
65 CCACCATATC
*
16839110 TTGGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGAT
1 TT-GAATATAAA-GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTAAT
*
16839175 TCCACCGTATC
64 TCCACCATATC
* * * *
16839186 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGAA-
1 TTGAATAT-AAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCT-AAT
16839250 TCCACC
64 TCCACC
16839256 GATAACGGAT
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
75 62 0.47
76 70 0.53
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (74 bp):
TTGAATATAAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTAATTC
CACCATATC
Found at i:16839163 original size:33 final size:34
Alignment explanation
Indices: 16839125--16839258 Score: 137
Period size: 33 Copynumber: 3.8 Consensus size: 34
16839115 ATATAAAGGG
16839125 GGTTGCTAAGTGCTGATTCC-CCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCACCGATTCATTGGT
* *
16839158 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCG-A--TT-CAT-TG---GT
* *
16839200 GGTTGCTAAGTGCTGATTCC-CCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCACCGATTCATTGGT
*
16839233 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCCACCGAT
16839259 AACGGATAAC
Statistics
Matches: 83, Mismatches: 8, Indels: 19
0.75 0.07 0.17
Matches are distributed among these distances:
33 40 0.48
34 7 0.08
35 1 0.01
36 2 0.02
37 3 0.04
38 3 0.04
39 2 0.02
40 1 0.01
41 3 0.04
42 21 0.25
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (34 bp):
GGTTGCTAAGTGCTGATTCCACCGATTCATTGGT
Found at i:16839246 original size:75 final size:75
Alignment explanation
Indices: 16839030--16839256 Score: 314
Period size: 75 Copynumber: 3.0 Consensus size: 75
16839020 ATAAGCTGGA
* * * *
16839030 GTATATTG-AATATAAAAGGGGTTGCTAAGTGCTAATTTCCTGATTCATTGGTGGTTGCTAAGTG
1 GTATCTTGAAATAT-AAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTG
*
16839094 CTAATTCCACC
65 CTGATTCCACC
* *
16839105 ATATCTTGGAATATAAAGGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTG
1 GTATCTTGAAATATAAA-GGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTG
16839170 CTGATTCCACC
65 CTGATTCCACC
* * *
16839181 GTATCTT-AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTG
1 GTATCTTGAAATAT-AAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTG
*
16839245 CTGAATCCACC
65 CTGATTCCACC
16839256 G
1 G
16839257 ATAACGGATA
Statistics
Matches: 137, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
75 69 0.50
76 68 0.50
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (75 bp):
GTATCTTGAAATATAAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGC
TGATTCCACC
Found at i:16839312 original size:2 final size:2
Alignment explanation
Indices: 16839305--16839360 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
16839295 GAAAAGATGA
16839305 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16839347 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
16839361 GGTGGATAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16841442 original size:11 final size:11
Alignment explanation
Indices: 16841402--16841477 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
16841392 ATTCTAAATA
*
16841402 TAATATTATTT
1 TAATATTAATT
16841413 TAATAGTTTAATAT
1 TAATA--TTAAT-T
16841427 TAATATTAATT
1 TAATATTAATT
16841438 TAATACTT-ATCT
1 TAATA-TTAAT-T
* *
16841450 TAGTAGT-ATT
1 TAATATTAATT
16841460 T--TATTAATT
1 TAATATTAATT
16841469 TAATATTAA
1 TAATATTAA
16841478 AGTGATTATC
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 2 0.04
11 22 0.42
12 12 0.23
13 4 0.08
14 6 0.11
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Found at i:16842563 original size:20 final size:20
Alignment explanation
Indices: 16842538--16842590 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
16842528 AAAAAAATCA
*
16842538 ATTGAAACTAAGAACAAATG
1 ATTGAAACCAAGAACAAATG
*
16842558 ATTGAAACCAAGAACAATTG
1 ATTGAAACCAAGAACAAATG
*
16842578 ATTAAAACCAAGA
1 ATTGAAACCAAGA
16842591 GTAAAAAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.19
Consensus pattern (20 bp):
ATTGAAACCAAGAACAAATG
Found at i:16842701 original size:20 final size:20
Alignment explanation
Indices: 16842676--16842713 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16842666 AACAACTTAT
16842676 TAAACAAACTTAAGAACTAC
1 TAAACAAACTTAAGAACTAC
*
16842696 TAAACAAACTTAATAACT
1 TAAACAAACTTAAGAACT
16842714 GCCTAGCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.24
Consensus pattern (20 bp):
TAAACAAACTTAAGAACTAC
Found at i:16849810 original size:28 final size:30
Alignment explanation
Indices: 16849779--16849846 Score: 113
Period size: 28 Copynumber: 2.3 Consensus size: 30
16849769 TAGGGTTTGT
*
16849779 TTTTTTATATATTATAGTTTTT-TTTA-TA
1 TTTTTTATATATTATAGTTTTTATATATTA
16849807 TTTTTTATATATTATAGTTTTTATATATTA
1 TTTTTTATATATTATAGTTTTTATATATTA
16849837 TTTTTTATAT
1 TTTTTTATAT
16849847 TAATTCTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
28 22 0.59
29 3 0.08
30 12 0.32
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (30 bp):
TTTTTTATATATTATAGTTTTTATATATTA
Found at i:16849827 original size:16 final size:16
Alignment explanation
Indices: 16849780--16849846 Score: 83
Period size: 16 Copynumber: 4.6 Consensus size: 16
16849770 AGGGTTTGTT
16849780 TTTTTATATATTATAG
1 TTTTTATATATTATAG
*
16849796 -TTTT-T-T-TTATAT
1 TTTTTATATATTATAG
16849808 TTTTTATATATTATAG
1 TTTTTATATATTATAG
16849824 TTTTTATATATTAT--
1 TTTTTATATATTATAG
16849838 TTTTTATAT
1 TTTTTATAT
16849847 TAATTCTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
12 5 0.11
13 5 0.11
14 11 0.24
15 5 0.11
16 19 0.42
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTTATATATTATAG
Found at i:16849856 original size:28 final size:27
Alignment explanation
Indices: 16849778--16849857 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 27
16849768 TTAGGGTTTG
*
16849778 TTTTTTTATATATTATAGTTTTTTTTATA
1 TTTTTTT-TATATTATA-TTTTTTATATA
* *
16849807 TTTTTTATATATTATAGTTTTTATATA
1 TTTTTTTTATATTATATTTTTTATATA
16849834 TTATTTTTTATATTA-ATTCTTTTA
1 TT-TTTTTTATATTATATT-TTTTA
16849858 CACTTTTTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
27 13 0.30
28 25 0.57
29 6 0.14
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (27 bp):
TTTTTTTTATATTATATTTTTTATATA
Found at i:16849857 original size:14 final size:12
Alignment explanation
Indices: 16849798--16849848 Score: 50
Period size: 11 Copynumber: 4.0 Consensus size: 12
16849788 TATTATAGTT
16849798 TTTTTTATATT-
1 TTTTTTATATTA
*
16849809 TTTTATATATTATA
1 TTTTTTATA-T-TA
16849823 GTTTTTATATATTA
1 -TTTTT-TATATTA
16849837 TTTTTTATATTA
1 TTTTTTATATTA
16849849 ATTCTTTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
11 8 0.24
12 8 0.24
13 6 0.18
14 2 0.06
15 5 0.15
16 4 0.12
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (12 bp):
TTTTTTATATTA
Found at i:16851513 original size:29 final size:28
Alignment explanation
Indices: 16851468--16851544 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 28
16851458 TTTGATCCAA
*
16851468 TGTGCAATTTGATACATAATA-TTTGATTT
1 TGTGCAATTT-ACACATAA-ACTTTGATTT
16851497 TGTGCAATTATACACATTAAACTTTGATTT
1 TGTGCAATT-TACACA-TAAACTTTGATTT
*
16851527 TGATTCAATTGTACACAT
1 TG-TGCAATT-TACACAT
16851545 TTAAAGAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 14 0.34
30 15 0.37
31 12 0.29
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (28 bp):
TGTGCAATTTACACATAAACTTTGATTT
Found at i:16851964 original size:18 final size:20
Alignment explanation
Indices: 16851927--16851964 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16851917 AGAGTTAATT
*
16851927 TATTATTGTTTGATATATTA
1 TATTATTGTTTGATACATTA
16851947 TATTATT-TTTGA-ACATTA
1 TATTATTGTTTGATACATTA
16851965 ATCTTATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.32, C:0.03, G:0.08, T:0.58
Consensus pattern (20 bp):
TATTATTGTTTGATACATTA
Found at i:16852579 original size:17 final size:16
Alignment explanation
Indices: 16852543--16852584 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
16852533 AATTTTTTTA
16852543 TATTTAAAA-ATAAAT
1 TATTTAAAATATAAAT
*
16852558 AATTTAAAATATTAAAT
1 TATTTAAAATA-TAAAT
16852575 TATTTAAAAT
1 TATTTAAAAT
16852585 TGGTTCCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 14 0.61
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTTAAAATATAAAT
Found at i:16854005 original size:64 final size:64
Alignment explanation
Indices: 16853860--16854024 Score: 183
Period size: 64 Copynumber: 2.6 Consensus size: 64
16853850 CATGCGGCCC
* * * * *
16853860 TACACGACCT-GACACATGCCCGTGTCCTTGGCCCGTGTGATCATTATCTTATAATTAGTGAGT
1 TACACGACCTAGACACACGTCTGTGTCCTTGGCCCGTGAGATCATTATCTTATAATCAGTGAGT
* * * *
16853923 TACACGACCTAGATACACG-CTTGTGTCCTTAGCCCGTGAGATCCTTATCTTGTAATCAGTGAGT
1 TACACGACCTAGACACACGTC-TGTGTCCTTGGCCCGTGAGATCATTATCTTATAATCAGTGAGT
* * *
16853987 TACATGGCCT-GAACACACGTCTGTCTCCTTGGCCCGTG
1 TACACGACCTAG-ACACACGTCTGTGTCCTTGGCCCGTG
16854025 TGAACCCTGC
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
63 12 0.14
64 72 0.85
65 1 0.01
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.30
Consensus pattern (64 bp):
TACACGACCTAGACACACGTCTGTGTCCTTGGCCCGTGAGATCATTATCTTATAATCAGTGAGT
Found at i:16855446 original size:8 final size:9
Alignment explanation
Indices: 16855424--16855448 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
16855414 CAAGTTTTTA
16855424 TAAAAATAT
1 TAAAAATAT
16855433 TAAAAATAT
1 TAAAAATAT
16855442 TAAAAAT
1 TAAAAAT
16855449 GATTTAAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
TAAAAATAT
Found at i:16858810 original size:25 final size:26
Alignment explanation
Indices: 16858755--16858814 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
16858745 TATATATTTT
*
16858755 TATATATATTTTATAATTCACATATA
1 TATACATATTTTATAATTCACATATA
* * * *
16858781 CATACATATTTT-TAATTTATATCTA
1 TATACATATTTTATAATTCACATATA
16858806 TATACATAT
1 TATACATAT
16858815 ATATCTCTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
25 18 0.64
26 10 0.36
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (26 bp):
TATACATATTTTATAATTCACATATA
Found at i:16859327 original size:70 final size:70
Alignment explanation
Indices: 16859194--16859326 Score: 205
Period size: 70 Copynumber: 1.9 Consensus size: 70
16859184 CAAACTCAAG
* ** *
16859194 TTTTAAACGATCTCGAGAATTATGAGGAGATCATGTCCTAACTTACTGGGCATGATCCCTTTTTC
1 TTTTAAACGATCTCGAGAATTAAGAAAAGATCATGTCCTAACTTACTAGGCATGATCCCTTTTTC
16859259 CCAAA
66 CCAAA
* *
16859264 TTTTAAACGATCTCGGGAATTAAGAAAAGATCGTGTCCTAACTTACTAGGCATGA-CCCTTTTT
1 TTTTAAACGATCTCGAGAATTAAGAAAAGATCATGTCCTAACTTACTAGGCATGATCCCTTTTT
16859327 TTTAAATCTG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 8 0.14
70 49 0.86
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.33
Consensus pattern (70 bp):
TTTTAAACGATCTCGAGAATTAAGAAAAGATCATGTCCTAACTTACTAGGCATGATCCCTTTTTC
CCAAA
Found at i:16861203 original size:24 final size:24
Alignment explanation
Indices: 16861174--16861221 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
16861164 AAATTAATAA
16861174 GTCAAATAAACTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
* *
16861198 GTCAAATATATTATACTAATAAAT
1 GTCAAATAAACTATACTAATAAAT
16861222 ACTAAATCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
GTCAAATAAACTATACTAATAAAT
Found at i:16865953 original size:26 final size:26
Alignment explanation
Indices: 16865905--16866011 Score: 133
Period size: 26 Copynumber: 4.1 Consensus size: 26
16865895 AATACACCAA
* ** *
16865905 TATCGCAGCAAAGCTACTGGTAATAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
* * *
16865931 TATCGTAACAAAGCTGCGAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
16865957 TATCACAGCAAAGCTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
*
16865983 TATCGCAGCAAAGTTGCCAGTAACAG
1 TATCGCAGCAAAGCTGCCAGTAACAG
16866009 TAT
1 TAT
16866012 ACTTCCTTCA
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 69 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAGTAACAG
Found at i:16866315 original size:27 final size:27
Alignment explanation
Indices: 16866176--16866316 Score: 162
Period size: 27 Copynumber: 5.2 Consensus size: 27
16866166 GGTATAACAG
*
16866176 TCATTTTACCCTATGAGGGG-ATTTCGG
1 TCATTTTACCCTAT-AGGGGTATTTCGA
* *
16866203 CCATCTTACCCTAT-GAGGGTATTTCGA
1 TCATTTTACCCTATAG-GGGTATTTCGA
* *
16866230 TGATTTTACCCTATGGGGGTATCTT-GA
1 TCATTTTACCCTATAGGGGTAT-TTCGA
* *
16866257 TCATCTTACCCTATAGGGGTATTTCGG
1 TCATTTTACCCTATAGGGGTATTTCGA
*
16866284 TCATTTTACCCTATAGGGGTATTTCAA
1 TCATTTTACCCTATAGGGGTATTTCGA
16866311 TCATTT
1 TCATTT
16866317 ATTGACCTTT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
25 1 0.01
26 5 0.05
27 87 0.91
28 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.39
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGGTATTTCGA
Found at i:16872579 original size:2 final size:2
Alignment explanation
Indices: 16872572--16872604 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16872562 NNNNNNNNAC
16872572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16872605 AAGCTGCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16872849 original size:15 final size:15
Alignment explanation
Indices: 16872831--16872860 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16872821 CGGTTGACTC
16872831 TTAATCGCACTATTA
1 TTAATCGCACTATTA
16872846 TTAATCGCACTATTA
1 TTAATCGCACTATTA
16872861 CTCTCCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (15 bp):
TTAATCGCACTATTA
Found at i:16874612 original size:15 final size:16
Alignment explanation
Indices: 16874584--16874613 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16874574 AATTAAATAC
16874584 AACAACATTTATTAAT
1 AACAACATTTATTAAT
16874600 AACAACA-TTATTAA
1 AACAACATTTATTAA
16874614 GTTGAAACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (16 bp):
AACAACATTTATTAAT
Found at i:16875124 original size:21 final size:20
Alignment explanation
Indices: 16875100--16875153 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
16875090 AATAAAAAGG
16875100 ATAAATTTTAAAACAATGTTA
1 ATAAATTTTAAAAC-ATGTTA
* *
16875121 ATAAACTCT-AAACATGTTA
1 ATAAATTTTAAAACATGTTA
16875140 ATAATAATTTTAAA
1 AT-A-AATTTTAAA
16875154 TAACGATGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
19 8 0.31
20 5 0.19
21 11 0.42
22 2 0.08
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.37
Consensus pattern (20 bp):
ATAAATTTTAAAACATGTTA
Found at i:16877608 original size:17 final size:18
Alignment explanation
Indices: 16877581--16877614 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
16877571 ATAAAAGTAG
*
16877581 AAAAATCAAATTGTATAA
1 AAAAATCAAATTATATAA
16877599 AAAAAT-AAATTATATA
1 AAAAATCAAATTATATA
16877615 GTTCAAATCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAAATCAAATTATATAA
Found at i:16880566 original size:2 final size:2
Alignment explanation
Indices: 16880561--16880593 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
16880551 TTTTTTAGTT
16880561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
16880594 GTTGTGATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16889074 original size:34 final size:33
Alignment explanation
Indices: 16889031--16889148 Score: 130
Period size: 34 Copynumber: 3.5 Consensus size: 33
16889021 GGATACACGG
16889031 GTAACTACACCACACCAGATTGCTCCTTACAGTA
1 GTAACTACACCACACCAGATTGCT-CTTACAGTA
* *
16889065 GTAACTACACCACACCAGATTGCTTGTTAGAGTA
1 GTAACTACACCACACCAGATTGC-TCTTACAGTA
* * ** *
16889099 ATAACTAAACCACACCAG-TTGCTCTGGCGAGCA
1 GTAACTACACCACACCAGATTGCTCTTAC-AGTA
*
16889132 GTAACTACACCTCACCA
1 GTAACTACACCACACCA
16889149 ACGCATTGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
32 2 0.03
33 21 0.30
34 46 0.66
35 1 0.01
ACGTcount: A:0.33, C:0.31, G:0.14, T:0.22
Consensus pattern (33 bp):
GTAACTACACCACACCAGATTGCTCTTACAGTA
Found at i:16893069 original size:29 final size:29
Alignment explanation
Indices: 16893019--16893078 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
16893009 GAAACTCTTC
* *
16893019 GGACCATGTAAGTCATCTTATCTATTAGA
1 GGACCATGTAAGTAATCCTATCTATTAGA
16893048 GGACCATGTAAGTAATCCTATCTATTAGA
1 GGACCATGTAAGTAATCCTATCTATTAGA
16893077 GG
1 GG
16893079 TATTCACAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (29 bp):
GGACCATGTAAGTAATCCTATCTATTAGA
Found at i:16898577 original size:24 final size:25
Alignment explanation
Indices: 16898548--16898597 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
16898538 GAGAGGAAAG
16898548 TTTAAAGAACATAAAA-GAAAAAAA
1 TTTAAAGAACATAAAACGAAAAAAA
** *
16898572 TTTAAATTACTTAAAACGAAAAAAA
1 TTTAAAGAACATAAAACGAAAAAAA
16898597 T
1 T
16898598 ATGGAGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (25 bp):
TTTAAAGAACATAAAACGAAAAAAA
Found at i:16900034 original size:112 final size:111
Alignment explanation
Indices: 16899675--16900037 Score: 403
Period size: 113 Copynumber: 3.2 Consensus size: 111
16899665 CCTGAACAAC
* * *
16899675 TAGTGGCGTTTCTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCATTTA-TTGTAAGCGCCGC
1 TAGTGGCGTTTC-GATAAAACGCCGTAAAAGAACAT-ATTAGTGGCGTTTATTTGTAAGCGCCGC
* *
16899739 AAAATACCTTAACCAAAACGCAGCGTTTGG-TTCAATTGTATATTAGAAT
64 -AAATACCTTAACCAAAACGCAGCGTTTGGTTTCGA-GGTATATTAGAAT
* * * ****
16899788 TAGTGGCGTTTTCGATAAAATGCCGCT-AAAGAATAGTATTAGCGGCGTTT-TACAAAAAGCGCC
1 TAGTGGCG-TTTCGATAAAACGCCG-TAAAAGAACA-TATTAGTGGCGTTTAT-TTGTAAGCGCC
* * * * *
16899851 GCAAATATCTTAACGAAAACGCAGCGTTTGGTCTCGAGGTAGATTAGTAT
62 GCAAATACCTTAACCAAAACGCAGCGTTTGGTTTCGAGGTATATTAGAAT
** *
16899901 TAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTATTTGTAAGCG-CGC
1 TAGTGGCGTTTCGATA-AAACGCCGTAAAAGAACAT-ATTAGTGGCGTTTATTTGTAAGCGCCGC
*
16899965 AAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGAAT
64 AAATACCTTAACCAAAACGCAGCGTTTGGTTTCGAGGTATATTAGAAT
16900013 TAGTGGCGTTTACGATAAAACGCCG
1 TAGTGGCGTTT-CGATAAAACGCCG
16900038 CAAATATCTT
Statistics
Matches: 203, Mismatches: 36, Indels: 23
0.77 0.14 0.09
Matches are distributed among these distances:
112 71 0.35
113 113 0.56
114 19 0.09
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (111 bp):
TAGTGGCGTTTCGATAAAACGCCGTAAAAGAACATATTAGTGGCGTTTATTTGTAAGCGCCGCAA
ATACCTTAACCAAAACGCAGCGTTTGGTTTCGAGGTATATTAGAAT
Found at i:16900145 original size:186 final size:188
Alignment explanation
Indices: 16899825--16900226 Score: 650
Period size: 186 Copynumber: 2.1 Consensus size: 188
16899815 AAAGAATAGT
* * *
16899825 ATTAGCGGCGTTTTAC-A-AAAAGCGCCGCAAATATCTTAACGAAAACGCAGCGTTTGGTCTCGA
1 ATTAGTGGCG-TTTACGATAAAA-CGCCGCAAATATCTTAACAAAAACGCACCGTTTGGTCTCGA
* * *
16899888 GGTAGATTAGTATTAGTGGCGTTTTTAAACAAACGCCGTAAAAGAACATCATTAGTGGCGTTTAT
64 GGTAGATTAGTATTAGTGGCGTTATTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTAT
*
16899953 TTGTAAGCG-CGC-AAATACCTTAACCAAAACGCAGCGTTTGGTTTTGAGGTATATTAGA
129 TTGTAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGCTTGGTTTTGAGGTATATTAGA
*
16900011 ATTAGTGGCGTTTACGATAAAACGCCGCAAATATCTTAACAAAAACGCACCGTTTGGTCTTGAGG
1 ATTAGTGGCGTTTACGATAAAACGCCGCAAATATCTTAACAAAAACGCACCGTTTGGTCTCGAGG
* *
16900076 TAGATTAGTTTTAGTGGCGTTATTAAAAAAATGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
66 TAGATTAGTATTAGTGGCGTTATTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
16900141 GTAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGCTTGGTTTTGAGGTATATTAGA
131 GTAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGCTTGGTTTTGAGGTATATTAGA
* *
16900199 ATTAGTGGCGTTTATGGTAAAACGCCGC
1 ATTAGTGGCGTTTACGATAAAACGCCGC
16900227 TAAAGAATAG
Statistics
Matches: 200, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
185 5 0.03
186 117 0.58
187 7 0.04
188 71 0.35
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (188 bp):
ATTAGTGGCGTTTACGATAAAACGCCGCAAATATCTTAACAAAAACGCACCGTTTGGTCTCGAGG
TAGATTAGTATTAGTGGCGTTATTAAAAAAACGCCGTAAAAGAACATAATTAGTGGCGTTTATTT
GTAAGCGCCGCAAAATACCTTAACCAAAACGCAGCGCTTGGTTTTGAGGTATATTAGA
Found at i:16900232 original size:114 final size:114
Alignment explanation
Indices: 16900033--16900269 Score: 259
Period size: 114 Copynumber: 2.1 Consensus size: 114
16900023 TACGATAAAA
* * **
16900033 CGCCGC-AAATATCTTAACAAAAACGCACCGTTTGGTCTTGAGGTAGATTAGTTTTAGTGGCGTT
1 CGCCGCAAAATACCTTAACAAAAACGCACCGCTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
* * * *
16900097 ATTAAAAAAATGCCGTAAAAGAACA-TAATTAGTGGCGTTTATT-TGTAAG
66 ATTAAAAAAACGCCGTAAAAGAACAGT-ATTAGCGGCGTTT-TTGGGAAAG
* * * *
16900146 CGCCGCAAAATACCTTAACCAAAACGCAGCGCTTGGTTTTGAGGTATATTAGAATTAGTGGCGTT
1 CGCCGCAAAATACCTTAACAAAAACGCACCGCTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
*** *
16900211 -TATGGTAAAACGCCGCT-AAAGAATAGTATTAGCGGCGTTTTTGGGAAAG
66 AT-TAAAAAAACGCCG-TAAAAGAACAGTATTAGCGGCGTTTTTGGGAAAG
16900260 CGCCGCAAAA
1 CGCCGCAAAA
16900270 CTACTTCATC
Statistics
Matches: 103, Mismatches: 16, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
113 9 0.09
114 92 0.89
115 2 0.02
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.28
Consensus pattern (114 bp):
CGCCGCAAAATACCTTAACAAAAACGCACCGCTTGGTCTTGAGGTAGATTAGAATTAGTGGCGTT
ATTAAAAAAACGCCGTAAAAGAACAGTATTAGCGGCGTTTTTGGGAAAG
Found at i:16909658 original size:12 final size:12
Alignment explanation
Indices: 16909641--16909678 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
16909631 CAGATGCCGT
16909641 AGCGAGAGAAGC
1 AGCGAGAGAAGC
16909653 AGCGAGAGAAGC
1 AGCGAGAGAAGC
*
16909665 AGCGATAGAAGC
1 AGCGAGAGAAGC
16909677 AG
1 AG
16909679 AGGTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.42, C:0.16, G:0.39, T:0.03
Consensus pattern (12 bp):
AGCGAGAGAAGC
Found at i:16910196 original size:85 final size:84
Alignment explanation
Indices: 16910103--16910297 Score: 220
Period size: 85 Copynumber: 2.3 Consensus size: 84
16910093 TTTGTGAAAC
*
16910103 AAGCGCCGCTAAAGAACACT-A-CTTTTAGCGAC-ATTTTTGAAC-AAGCGCCGCTATAGAACAT
1 AAGCGCCGCTAAAGAACA-TGATC-TTTAGCGACGATTTTT--ACTAAGCGCCGCTAAAGAACAT
*
16910164 TA-CTTTTAGAGGCGTTTTCTTCCA
62 GATC-TTTAGAGGCGTTTT-TTCCA
* * *
16910188 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTTCTAAGCGCCGCTAAAGAACATGATC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGACGATTTTTACTAAGCGCCGCTAAAGAACATGATC
* *
16910253 TTTAGTGGCGTTTTTTCCT
66 TTTAGAGGCGTTTTTTCCA
**
16910272 AAGCGCCATTAAAGAACATGATCTTT
1 AAGCGCCGCTAAAGAACATGATCTTT
16910298 TGCGGCGTTT
Statistics
Matches: 96, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
84 30 0.31
85 59 0.61
86 7 0.07
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGACGATTTTTACTAAGCGCCGCTAAAGAACATGATC
TTTAGAGGCGTTTTTTCCA
Found at i:16910241 original size:42 final size:42
Alignment explanation
Indices: 16910103--16910310 Score: 219
Period size: 42 Copynumber: 4.9 Consensus size: 42
16910093 TTTGTGAAAC
* * **
16910103 AAGCGCCGCTAAAGAACACT-A-CTTTTAGCGACATTTTTGAAC-
1 AAGCGCCGCTAAAGAACA-TGATC-TTTAGCGGCGTTTTT-TCCT
* * * *
16910145 AAGCGCCGCTATAGAACATTA-CTTTTAGAGGCGTTTTCTTCCA
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTT-TTCCT
16910188 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTTT-CT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTTTCCT
*
16910230 AAGCGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCT
** *
16910272 AAGCGCCATTAAAGAACATGATCTTTTGCGGCGTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT
16910311 TCTGTAAGCG
Statistics
Matches: 145, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
41 7 0.05
42 102 0.70
43 31 0.21
44 5 0.03
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCT
Found at i:16910310 original size:84 final size:86
Alignment explanation
Indices: 16910145--16910322 Score: 245
Period size: 84 Copynumber: 2.1 Consensus size: 86
16910135 ATTTTTGAAC
* * *
16910145 AAGCGCCGCTATAGAACATTACTTTTAGAGGCGTTTTCTTCCAAAGCGCCGCTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGACTTTTAGAGGCGTTTTCTTCCAAAGCGCCACTAAAGAACATGAT
16910210 CTTTAGCGGCGCTTTTTTC-T
66 CTTTAGCGGCGCTTTTTTCGT
* * *
16910230 AAGCGCCGCTAAAGAACATGA-TCTTTAGTGGCGTTTT-TTCCTAAGCGCCATTAAAGAACATGA
1 AAGCGCCGCTAAAGAACATGACT-TTTAGAGGCGTTTTCTTCCAAAGCGCCACTAAAGAACATGA
* *
16910293 TCTTTTGCGGCGTTTTTTTCTGT
65 TCTTTAGCGGCGCTTTTTTC-GT
16910316 AAGCGCC
1 AAGCGCC
16910323 ACAAAAGTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
84 42 0.51
85 32 0.39
86 8 0.10
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.33
Consensus pattern (86 bp):
AAGCGCCGCTAAAGAACATGACTTTTAGAGGCGTTTTCTTCCAAAGCGCCACTAAAGAACATGAT
CTTTAGCGGCGCTTTTTTCGT
Found at i:16912458 original size:12 final size:13
Alignment explanation
Indices: 16912432--16912460 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16912422 GAATATATCA
16912432 AAATATCACCAAT
1 AAATATCACCAAT
16912445 AAATATCA-CAAT
1 AAATATCACCAAT
16912457 AAAT
1 AAAT
16912461 CTATCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.59, C:0.17, G:0.00, T:0.24
Consensus pattern (13 bp):
AAATATCACCAAT
Found at i:16916901 original size:18 final size:18
Alignment explanation
Indices: 16916855--16916901 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
16916845 TAATTTTTCG
*
16916855 TAATATTTTTATAATTTT
1 TAATAATTTTATAATTTT
* *
16916873 TCATAACTTTATAATTTT
1 TAATAATTTTATAATTTT
*
16916891 TAATGATTTTA
1 TAATAATTTTA
16916902 AATAGAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (18 bp):
TAATAATTTTATAATTTT
Found at i:16918860 original size:24 final size:24
Alignment explanation
Indices: 16918812--16918858 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
16918802 ATTGGTCATA
* *
16918812 GAGAGATTTGAGGAGGGATATTTG
1 GAGAGATTTGAAGAGGAATATTTG
16918836 GAGAGATTTGAAGAGAGAATATT
1 GAGAGATTTGAAGAG-GAATATT
16918859 GGGATTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (24 bp):
GAGAGATTTGAAGAGGAATATTTG
Found at i:16919162 original size:27 final size:27
Alignment explanation
Indices: 16919131--16919332 Score: 151
Period size: 27 Copynumber: 7.8 Consensus size: 27
16919121 GTTATGACCT
*
16919131 AAATACCCTCATAGGGTAGAATGATCG
1 AAATACCCTCATAGGGTAAAATGATCG
* * *
16919158 AAATACCCTTATAGGGTAAAATAACCG
1 AAATACCCTCATAGGGTAAAATGATCG
*
16919185 AAATA----C---GGGTAAAATCG-TCA
1 AAATACCCTCATAGGGTAAAAT-GATCG
* * *
16919205 AAATACCCTCACAAGGTAAAATGACCG
1 AAATACCCTCATAGGGTAAAATGATCG
* *
16919232 AAATACCCCCACAGGGTAAAATGATCG
1 AAATACCCTCATAGGGTAAAATGATCG
* *
16919259 AAATACCC-CTAAAAGGTAAAATGA-CTG
1 AAATACCCTC-ATAGGGTAAAATGATC-G
* *
16919286 AAATA--CTTATAGGTTAAAATGA-CTG
1 AAATACCCTCATAGGGTAAAATGATC-G
16919311 AAATACCCTCATAGGGTAAAAT
1 AAATACCCTCATAGGGTAAAAT
16919333 AACTGTTATA
Statistics
Matches: 139, Mismatches: 22, Indels: 28
0.74 0.12 0.15
Matches are distributed among these distances:
20 15 0.11
24 1 0.01
25 20 0.14
26 3 0.02
27 100 0.72
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.21
Consensus pattern (27 bp):
AAATACCCTCATAGGGTAAAATGATCG
Found at i:16919272 original size:74 final size:74
Alignment explanation
Indices: 16919131--16919272 Score: 176
Period size: 74 Copynumber: 1.9 Consensus size: 74
16919121 GTTATGACCT
* * * * ** * ***
16919131 AAATACCCTCATAGGGTAGAATGATCGAAATACCCTTATAGGGTAAAATAACCGAAATACGGGTA
1 AAATACCCTCACAAGGTAAAATGACCGAAATACCCCCACAGGGTAAAATAACCGAAATACCCCTA
16919196 AAATCGTCA
66 AAATCGTCA
* *
16919205 AAATACCCTCACAAGGTAAAATGACCGAAATACCCCCACAGGGTAAAATGATCGAAATACCCCTA
1 AAATACCCTCACAAGGTAAAATGACCGAAATACCCCCACAGGGTAAAATAACCGAAATACCCCTA
16919270 AAA
66 AAA
16919273 GGTAAAATGA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
74 56 1.00
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (74 bp):
AAATACCCTCACAAGGTAAAATGACCGAAATACCCCCACAGGGTAAAATAACCGAAATACCCCTA
AAATCGTCA
Found at i:16936697 original size:26 final size:26
Alignment explanation
Indices: 16936668--16936718 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
16936658 TGAGCTTTCC
**
16936668 AATGTGCAAGCTGTAAGCTCAGCAAA
1 AATGTGCAAGCTACAAGCTCAGCAAA
* *
16936694 AATGTGTAAGTTACAAGCTCAGCAA
1 AATGTGCAAGCTACAAGCTCAGCAA
16936719 GATGTCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.22
Consensus pattern (26 bp):
AATGTGCAAGCTACAAGCTCAGCAAA
Found at i:16938889 original size:57 final size:60
Alignment explanation
Indices: 16938796--16938943 Score: 178
Period size: 57 Copynumber: 2.5 Consensus size: 60
16938786 ACCCTAATTC
* * * *
16938796 GGATTACCCGTCCGGACTAAATCCATTTTCCACATATTCTTCGAGAGGACTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGAGAGGACTATATCAATA
* * *
16938854 -GATCACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTTGGGAGGGCTATATCAAGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGAGAGGACTATATC-A-ATA
16938915 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
16938944 ACCATCAATT
Statistics
Matches: 76, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
56 6 0.08
57 41 0.54
60 1 0.01
61 1 0.01
62 21 0.28
63 6 0.08
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGAGAGGACTATATCAATA
Found at i:16941127 original size:12 final size:12
Alignment explanation
Indices: 16941110--16941135 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16941100 TTGTCTTGTG
16941110 TTATGTTTTTCT
1 TTATGTTTTTCT
16941122 TTATGTTTTTCT
1 TTATGTTTTTCT
16941134 TT
1 TT
16941136 CTCTACTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (12 bp):
TTATGTTTTTCT
Found at i:16941644 original size:20 final size:21
Alignment explanation
Indices: 16941619--16941663 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
16941609 AGGCAAGCTT
16941619 ATTGGAC-CCAAAGTCGCAAC
1 ATTGGACACCAAAGTCGCAAC
*
16941639 ATTGGACGATCAAAGTCGCAAC
1 ATTGGAC-ACCAAAGTCGCAAC
16941661 ATT
1 ATT
16941664 AGCCTACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (21 bp):
ATTGGACACCAAAGTCGCAAC
Found at i:16941675 original size:21 final size:22
Alignment explanation
Indices: 16941627--16941683 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
16941617 TTATTGGACC
*
16941627 CAAAGTCGCAACATTGGACGAT
1 CAAAGTCGCAACATTAGACGAT
* *
16941649 CAAAGTCGCAACATTAGCCTA-
1 CAAAGTCGCAACATTAGACGAT
*
16941670 CAAAGTCGCGACAT
1 CAAAGTCGCAACAT
16941684 CCACTCACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.37, C:0.26, G:0.19, T:0.18
Consensus pattern (22 bp):
CAAAGTCGCAACATTAGACGAT
Found at i:16941783 original size:56 final size:56
Alignment explanation
Indices: 16941692--16941800 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
16941682 ATCCACTCAC
* *
16941692 CAAAGTCACAACATTCAAGCCAATAGCTTGAAGATGGAAGTTGATCCCAAACATAA
1 CAAAATCACAACATTCAAGCCAATAGCCTGAAGATGGAAGTTGATCCCAAACATAA
*
16941748 CAAAATCACAACATTCAAGCCAGTAGCCTGAAGATGGAAGTTGATCCCAAACA
1 CAAAATCACAACATTCAAGCCAATAGCCTGAAGATGGAAGTTGATCCCAAACA
16941801 GCAGCAAAGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (56 bp):
CAAAATCACAACATTCAAGCCAATAGCCTGAAGATGGAAGTTGATCCCAAACATAA
Found at i:16943299 original size:22 final size:22
Alignment explanation
Indices: 16943271--16943327 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
16943261 TTTATTGTTC
16943271 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
*
16943293 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTG
**
16943315 AGCCATGAGAGCT
1 AAACATGAGAGCT
16943328 ACTCTATTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:16950208 original size:20 final size:22
Alignment explanation
Indices: 16950192--16950233 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
16950182 CAAATTAAAG
16950192 CAAAATAAAAAAAATTAAATAC
1 CAAAATAAAAAAAATTAAATAC
16950214 CAAAATAAAAAAAA-TAAATA
1 CAAAATAAAAAAAATTAAATA
16950234 TAGTTGGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (22 bp):
CAAAATAAAAAAAATTAAATAC
Found at i:16950225 original size:21 final size:22
Alignment explanation
Indices: 16950192--16950233 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
16950182 CAAATTAAAG
*
16950192 CAAAATAAAAAAAATTAAATAC
1 CAAAATAAAAAAAAATAAATAC
16950214 CAAAAT-AAAAAAAATAAATA
1 CAAAATAAAAAAAAATAAATA
16950234 TAGTTGGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.17
Consensus pattern (22 bp):
CAAAATAAAAAAAAATAAATAC
Found at i:16950680 original size:12 final size:11
Alignment explanation
Indices: 16950642--16950678 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
16950632 ATTTTTTTAA
16950642 TTTTAAAATTT
1 TTTTAAAATTT
16950653 TTTTAAAATTT
1 TTTTAAAATTT
16950664 TTTTAAAATTT
1 TTTTAAAATTT
16950675 TTTT
1 TTTT
16950679 TATTTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:16950769 original size:31 final size:31
Alignment explanation
Indices: 16950731--16950791 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
16950721 CGGGTCAAGC
*
16950731 CGAGCTCGGGCTT-AGAAATTTTTTTCCGGGT
1 CGAGCTCGGGCTTAAG-AATTTTTTCCCGGGT
16950762 CGAGCTCGGGCTTAAGAATTTTTTCCCGGG
1 CGAGCTCGGGCTTAAGAATTTTTTCCCGGG
16950792 CCGGGCCTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.16, C:0.21, G:0.30, T:0.33
Consensus pattern (31 bp):
CGAGCTCGGGCTTAAGAATTTTTTCCCGGGT
Found at i:16959314 original size:31 final size:31
Alignment explanation
Indices: 16959253--16959316 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
16959243 ATCCTTAAAT
* *
16959253 TTGACAATTATTCTCATATTATGATTTGAAC
1 TTGACAATTATTCTCATATTAGGATCTGAAC
* *
16959284 TTGACAATTATT-TACATATTGGGGTCTGAAC
1 TTGACAATTATTCT-CATATTAGGATCTGAAC
16959315 TT
1 TT
16959317 TAGAGTATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.04
31 27 0.96
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (31 bp):
TTGACAATTATTCTCATATTAGGATCTGAAC
Found at i:16960680 original size:22 final size:22
Alignment explanation
Indices: 16960641--16960734 Score: 127
Period size: 22 Copynumber: 4.3 Consensus size: 22
16960631 ACAAATCCCA
*
16960641 TCTCAATTTCAC-TAAAAAATTC
1 TCTCAATTTC-CTTCAAAAATTC
*
16960663 TCTCAAATTCCTTCAAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
*
16960685 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCAAAAATTC
* *
16960707 TCACAATTTCCTTCAAAAAATC
1 TCTCAATTTCCTTCAAAAATTC
16960729 TCTCAA
1 TCTCAA
16960735 CTCCATATTA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
21 1 0.02
22 62 0.98
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCAATTTCCTTCAAAAATTC
Found at i:16960822 original size:26 final size:26
Alignment explanation
Indices: 16960771--16960820 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
16960761 CAATTTCATT
16960771 TTTTTAAGAAAATTTTAAATATTTTA
1 TTTTTAAGAAAATTTTAAATATTTTA
16960797 TTTTTAA-AATAATTTTAAA-ATTTT
1 TTTTTAAGAA-AATTTTAAATATTTT
16960821 TAATATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (26 bp):
TTTTTAAGAAAATTTTAAATATTTTA
Found at i:16960957 original size:26 final size:25
Alignment explanation
Indices: 16960909--16960962 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
16960899 GTATTAAATT
16960909 TAATTTTTATAAATTATTATTTAAGA
1 TAATTTTTATAAATTATTATTT-AGA
**
16960935 TAATTTTTATTTATGTATT-TTTAGA
1 TAATTTTTATAAAT-TATTATTTAGA
16960960 TAA
1 TAA
16960963 ATATTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.24
26 15 0.60
27 4 0.16
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (25 bp):
TAATTTTTATAAATTATTATTTAGA
Found at i:16963132 original size:23 final size:23
Alignment explanation
Indices: 16963102--16963181 Score: 115
Period size: 23 Copynumber: 3.5 Consensus size: 23
16963092 ATATTATTTG
16963102 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
16963125 ATTTAATTAAAAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCTA
* ****
16963148 ATTAAATTAAAAACCCCCGGCTA
1 ATTTAATTAAAAACCCTAACCTA
16963171 ATTTAATTAAA
1 ATTTAATTAAA
16963182 TTAAAAACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (23 bp):
ATTTAATTAAAAACCCTAACCTA
Found at i:16963214 original size:30 final size:30
Alignment explanation
Indices: 16963174--16963517 Score: 440
Period size: 30 Copynumber: 11.7 Consensus size: 30
16963164 CCGGCTAATT
*
16963174 TAATTAAATTAAAAACCCTAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
* *
16963204 TAATTTAATTAACAACCCTAAACTCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
*
16963234 TAATTTAATTAAAAACCCTAAACTCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
16963264 TAATTTAATTAAAAACCCT-AACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
* **
16963293 TAATTAAATTAAAAACCC----CCGGCTAATT
1 TAATTTAATTAAAAACCCTAAACC--CTAACC
*
16963321 TAATTAAATTAAAAACCCTAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
*
16963351 TAATTTAATTAACAACCCTAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
16963381 TAATTTAATTAAAAACCCT-AACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
* **
16963410 TAATTAAATTAAAAACCC----CCGGCTAATT
1 TAATTTAATTAAAAACCCTAAACC--CTAACC
*
16963438 TAATTAAATTAAAAACCCTAAACCCTAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
* *
16963468 TAATTTAATTAACAACCCT-AACCATAACC
1 TAATTTAATTAAAAACCCTAAACCCTAACC
16963497 TAATTTAATTAAAAACCCTAA
1 TAATTTAATTAAAAACCCTAA
16963518 CAAAAATTGA
Statistics
Matches: 279, Mismatches: 22, Indels: 26
0.85 0.07 0.08
Matches are distributed among these distances:
26 4 0.01
28 44 0.16
29 80 0.29
30 147 0.53
32 4 0.01
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.27
Consensus pattern (30 bp):
TAATTTAATTAAAAACCCTAAACCCTAACC
Found at i:16963350 original size:117 final size:115
Alignment explanation
Indices: 16963112--16963518 Score: 555
Period size: 117 Copynumber: 3.5 Consensus size: 115
16963102 ATTTAATTAA
*
16963112 AAACCCTAACCTAATTTAATTAAAAA--C---CCTAACCTAATTAAATTAAAAACCC---CCGGC
1 AAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACC--C
** ** * *
16963169 TAATTTAATTAAATTAAAAACCCTAAACC--CTAACCTAATTTAATTAACAACCCT
64 TAACCTAATTAAATTAAAAACCC----CCGGCTAATTTAATTAAATTAAAAACCCT
*
16963223 AAACTCTAACCTAATTTAATTAAAAACCCTAAACTCTAACCTAATTTAATTAAAAACCCTAACCC
1 AAACCCTAACCTAATTTAATTAAAAACCCT-AAC-CTAACCTAATTTAATTAAAAACCCTAACCC
16963288 TAACCTAATTAAATTAAAAACCCCCGGCTAATTTAATTAAATTAAAAACCCT
64 TAACCTAATTAAATTAAAAACCCCCGGCTAATTTAATTAAATTAAAAACCCT
*
16963340 AAACCCTAACCTAATTTAATTAACAACCCTAAACCCTAACCTAATTTAATTAAAAACCCTAACCC
1 AAACCCTAACCTAATTTAATTAAAAACCCT-AA-CCTAACCTAATTTAATTAAAAACCCTAACCC
16963405 TAACCTAATTAAATTAAAAACCCCCGGCTAATTTAATTAAATTAAAAACCCT
64 TAACCTAATTAAATTAAAAACCCCCGGCTAATTTAATTAAATTAAAAACCCT
*
16963457 AAACCCTAACCTAATTTAATTAACAACCCTAACCATAACCTAATTTAATTAAAAACCCTAAC
1 AAACCCTAACCTAATTTAATTAAAAACCCTAACC-TAACCTAATTTAATTAAAAACCCTAAC
16963519 AAAAATTGAT
Statistics
Matches: 272, Mismatches: 10, Indels: 23
0.89 0.03 0.08
Matches are distributed among these distances:
111 25 0.09
113 1 0.00
115 4 0.01
116 29 0.11
117 165 0.61
118 24 0.09
119 22 0.08
121 2 0.01
ACGTcount: A:0.46, C:0.26, G:0.01, T:0.27
Consensus pattern (115 bp):
AAACCCTAACCTAATTTAATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCCTA
ACCTAATTAAATTAAAAACCCCCGGCTAATTTAATTAAATTAAAAACCCT
Found at i:16963379 original size:147 final size:145
Alignment explanation
Indices: 16963113--16963517 Score: 560
Period size: 147 Copynumber: 2.8 Consensus size: 145
16963103 TTTAATTAAA
*
16963113 AACCCTAACCTAATTTAATT--AAA---AACCCTAACCTAATTAAATTAAAAACCCCCGGCTAAT
1 AACCCTAACCTAATTAAATTAAAAACCCAACCCTAACCTAATTAAATTAAAAACCCCCGGCTAAT
*
16963173 TTAATTAAATTAAAAACCCTAAACCCTAACCTAATTTAATTAACAACCCTAAACTCTAACCTAAT
66 TTAATTAAATTAAAAACCCTAAACCCTAACCTAATTTAATTAACAACCCTAAACCCTAACCTAAT
16963238 TTAATTAAAAACCCT
131 TTAATTAAAAACCCT
* *
16963253 AAACTCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTAAATTAAAAACCCCCGGCTA
1 -AACCCTAACCTAATTAAATTAAAAACCC-AACCCTAACCTAATTAAATTAAAAACCCCCGGCTA
16963318 ATTTAATTAAATTAAAAACCCTAAACCCTAACCTAATTTAATTAACAACCCTAAACCCTAACCTA
64 ATTTAATTAAATTAAAAACCCTAAACCCTAACCTAATTTAATTAACAACCCTAAACCCTAACCTA
16963383 ATTTAATTAAAAACCCT
129 ATTTAATTAAAAACCCT
**
16963400 AACCCTAACCTAATTAAATTAAAAACCC--CCGGCTAATTTAATTAAATTAAAAACCCTAAACC-
1 AACCCTAACCTAATTAAATTAAAAACCCAACC--CTAACCTAATTAAATTAAAAACCC----CCG
** * * * *
16963462 -CTAACCTAATTTAATTAACAACCCT-AACCATAACCTAATTTAATTAAAAACCCTAA
60 GCTAATTTAATTAAATTAAAAACCCTAAACCCTAACCTAATTTAATTAACAACCCTAA
16963518 CAAAAATTGA
Statistics
Matches: 240, Mismatches: 12, Indels: 19
0.89 0.04 0.07
Matches are distributed among these distances:
141 19 0.08
143 5 0.02
145 22 0.09
146 55 0.23
147 137 0.57
149 2 0.01
ACGTcount: A:0.46, C:0.25, G:0.01, T:0.27
Consensus pattern (145 bp):
AACCCTAACCTAATTAAATTAAAAACCCAACCCTAACCTAATTAAATTAAAAACCCCCGGCTAAT
TTAATTAAATTAAAAACCCTAAACCCTAACCTAATTTAATTAACAACCCTAAACCCTAACCTAAT
TTAATTAAAAACCCT
Found at i:16963413 original size:24 final size:23
Alignment explanation
Indices: 16963370--16963417 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
16963360 TAACAACCCT
**
16963370 AAACCCTAACCTAATTTAATTAA
1 AAACCCTAACCTAACCTAATTAA
16963393 AAACCCTAACCCTAACCTAATTAA
1 AAACCCTAA-CCTAACCTAATTAA
16963417 A
1 A
16963418 TTAAAAACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (23 bp):
AAACCCTAACCTAACCTAATTAA
Found at i:16969034 original size:20 final size:20
Alignment explanation
Indices: 16969011--16969048 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16969001 CTACCTGTAA
*
16969011 AAGTTCACTTCTACCCATTC
1 AAGTCCACTTCTACCCATTC
16969031 AAGTCCACTTCTACCCAT
1 AAGTCCACTTCTACCCAT
16969049 ACATCTTGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.37, G:0.05, T:0.32
Consensus pattern (20 bp):
AAGTCCACTTCTACCCATTC
Found at i:16971291 original size:15 final size:15
Alignment explanation
Indices: 16971263--16971301 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
16971253 ATATAAGCTA
16971263 AATA-CAAT-ATAAT
1 AATACCAATAATAAT
16971276 AATACCAATAATAAT
1 AATACCAATAATAAT
*
16971291 AATACTAATAA
1 AATACCAATAA
16971302 ACAAGGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 15 0.65
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (15 bp):
AATACCAATAATAAT
Found at i:16973055 original size:22 final size:23
Alignment explanation
Indices: 16973027--16973079 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
16973017 TTCGTGTAAC
16973027 TAAATTGTATAT-TTATATATTT
1 TAAATTGTATATGTTATATATTT
*
16973049 TAAATTG-A-ATGTTATGTATTT
1 TAAATTGTATATGTTATATATTT
*
16973070 GAAA-TGTATA
1 TAAATTGTATA
16973080 AGTGCCATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 4 0.15
21 14 0.54
22 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (23 bp):
TAAATTGTATATGTTATATATTT
Found at i:16973276 original size:25 final size:25
Alignment explanation
Indices: 16973241--16973289 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
16973231 CCATTATTAG
*
16973241 CTCTCATGAGCATCCCGATATATGT
1 CTCTCACGAGCATCCCGATATATGT
* *
16973266 CTCTCACGAGCTTCCCGTTATATG
1 CTCTCACGAGCATCCCGATATATG
16973290 GTTCTTGCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33
Consensus pattern (25 bp):
CTCTCACGAGCATCCCGATATATGT
Found at i:16973532 original size:24 final size:24
Alignment explanation
Indices: 16973378--16973574 Score: 80
Period size: 25 Copynumber: 7.8 Consensus size: 24
16973368 CAGCTCTTAT
* *
16973378 GAGCGTCCCGATATATGGCTCT-TCG
1 GAGCTTCCCGTTA-ATGGCTCTCT-G
* *
16973403 GAGCTTCCTGATTAAAGGCTCTTTCAT-
1 GAGCTTCCCG-TTAATGGCTC--TC-TG
16973430 GAGCTTCCCGATTAATTGGCTCTCTG
1 GAGCTTCCCG-TTAA-TGGCTCTCTG
* * *
16973456 GAGCTTCCCGATATTGGTTGGCT-TG
1 GAGCTTCCCGTTAATGGCT--CTCTG
* * * * *
16973481 AACCTTCCCGATATTGGCTCGTAT-
1 GAGCTTCCCGTTAATGGCTC-TCTG
*
16973505 GAGCTTCCCGTTAATGGATCTCTG
1 GAGCTTCCCGTTAATGGCTCTCTG
* * *
16973529 GAGCTTCCTGTTACATGGTTCACAT-
1 GAGCTTCCCGTTA-ATGGCTCTC-TG
*
16973554 GAGCTTCCCGTTTATGTGCTC
1 GAGCTTCCCGTTAATG-GCTC
16973575 CTATGAGCAT
Statistics
Matches: 133, Mismatches: 24, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
23 3 0.02
24 35 0.26
25 57 0.43
26 17 0.13
27 15 0.11
28 5 0.04
29 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.23, T:0.35
Consensus pattern (24 bp):
GAGCTTCCCGTTAATGGCTCTCTG
Found at i:16977179 original size:32 final size:31
Alignment explanation
Indices: 16977136--16977207 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
16977126 TTAAAATTTT
16977136 TATTTTAAAAAAATTA-TAAAAATTCTAAAAAC
1 TATTTTAAAAAAA--AGTAAAAATTCTAAAAAC
* *
16977168 TATTTTTAAAAAAAGTTAAAATTCTAAAAAC
1 TATTTTAAAAAAAAGTAAAAATTCTAAAAAC
*
16977199 T-TTCTAAAA
1 TATTTTAAAA
16977208 TAATAATTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 7 0.20
31 16 0.46
32 12 0.34
ACGTcount: A:0.56, C:0.07, G:0.01, T:0.36
Consensus pattern (31 bp):
TATTTTAAAAAAAAGTAAAAATTCTAAAAAC
Found at i:16977180 original size:34 final size:34
Alignment explanation
Indices: 16977115--16977199 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 34
16977105 TTCAAAATAT
* * *
16977115 TTATAAAAATT-TTAAAATTTTTATTTTAAAAAAA
1 TTATAAAAATTCTAAAAACTATTA-TTTAAAAAAA
16977149 TTATAAAAATTCTAAAAACTATT-TTTAAAAAAA
1 TTATAAAAATTCTAAAAACTATTATTTAAAAAAA
*
16977182 GT-T-AAAATTCTAAAAACT
1 TTATAAAAATTCTAAAAACT
16977200 TTCTAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
31 15 0.33
32 1 0.02
33 11 0.24
34 11 0.24
35 8 0.17
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (34 bp):
TTATAAAAATTCTAAAAACTATTATTTAAAAAAA
Found at i:16977189 original size:31 final size:33
Alignment explanation
Indices: 16977138--16977199 Score: 101
Period size: 31 Copynumber: 1.9 Consensus size: 33
16977128 AAAATTTTTA
*
16977138 TTTTAAAAAAATTATAAAAATTCTAAAAACTAT
1 TTTTAAAAAAAGTATAAAAATTCTAAAAACTAT
16977171 TTTTAAAAAAAGT-T-AAAATTCTAAAAACT
1 TTTTAAAAAAAGTATAAAAATTCTAAAAACT
16977200 TTCTAAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 15 0.54
32 1 0.04
33 12 0.43
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (33 bp):
TTTTAAAAAAAGTATAAAAATTCTAAAAACTAT
Found at i:16978537 original size:86 final size:86
Alignment explanation
Indices: 16978439--16978696 Score: 498
Period size: 86 Copynumber: 3.0 Consensus size: 86
16978429 TTTGGGCACC
16978439 AAAAATTTAAAAAAAATGCAAATTGAGCATTGCCATTAACAACCACTTTCATTTTAGTCACCTAA
1 AAAAATTTAAAAAAAATGCAAATTGAGCATTGCCATTAACAACCACTTTCATTTTAGTCACCTAA
16978504 TTACTTTAATAAGTTTTTATT
66 TTACTTTAATAAGTTTTTATT
16978525 AAAAATTTAAAAAAAATGCAAATTGAGCATTGCCATTAACAACCACTTTCATTTTAGTCACCTAA
1 AAAAATTTAAAAAAAATGCAAATTGAGCATTGCCATTAACAACCACTTTCATTTTAGTCACCTAA
16978590 TTACTTTAATAAGTTTTTATT
66 TTACTTTAATAAGTTTTTATT
* *
16978611 AAAAATTTTAAAAAAATGCAAATTGAGCATTGCCATTAACAACCATTTTCATTTTAGTCACCTAA
1 AAAAATTTAAAAAAAATGCAAATTGAGCATTGCCATTAACAACCACTTTCATTTTAGTCACCTAA
16978676 TTACTTTAATAAGTTTTTATT
66 TTACTTTAATAAGTTTTTATT
16978697 TTAGTCACTC
Statistics
Matches: 170, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 170 1.00
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (86 bp):
AAAAATTTAAAAAAAATGCAAATTGAGCATTGCCATTAACAACCACTTTCATTTTAGTCACCTAA
TTACTTTAATAAGTTTTTATT
Found at i:16980962 original size:10 final size:10
Alignment explanation
Indices: 16980947--16980975 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
16980937 ACATGGGTTC
16980947 AAGTGCATTG
1 AAGTGCATTG
16980957 AAGTGCATTG
1 AAGTGCATTG
16980967 AAGTGCATT
1 AAGTGCATT
16980976 ATCCTCCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.28, T:0.31
Consensus pattern (10 bp):
AAGTGCATTG
Found at i:16983874 original size:18 final size:18
Alignment explanation
Indices: 16983851--16983888 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
16983841 TGCCAGGTGC
*
16983851 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
16983869 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
16983887 GT
1 GT
16983889 TTCTTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:16984341 original size:25 final size:25
Alignment explanation
Indices: 16984307--16984354 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
16984297 AATAAAATAA
*
16984307 AATTTGTTTTTA-ATATTTTAATAGT
1 AATTTATTTTTATAT-TTTTAATAGT
16984332 AATTTATTTTTATATTTTTAATA
1 AATTTATTTTTATATTTTTAATA
16984355 TATTTGTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (25 bp):
AATTTATTTTTATATTTTTAATAGT
Found at i:16984432 original size:25 final size:25
Alignment explanation
Indices: 16984398--16984445 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
16984388 TAATAAAATA
*
16984398 AATTTGTTTTTAATATTT-TAATAGT
1 AATTTATTTTT-ATATTTCTAATAGT
16984423 AATTTATTTTTATATTTCTAATA
1 AATTTATTTTTATATTTCTAATA
16984446 AAATAGAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.60
Consensus pattern (25 bp):
AATTTATTTTTATATTTCTAATAGT
Found at i:16987653 original size:16 final size:16
Alignment explanation
Indices: 16987632--16987666 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
16987622 CAGAACCGTC
16987632 TTCTCAAAATTATTTT
1 TTCTCAAAATTATTTT
*
16987648 TTCTCATAATTATTTT
1 TTCTCAAAATTATTTT
16987664 TTC
1 TTC
16987667 AGGAACTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (16 bp):
TTCTCAAAATTATTTT
Found at i:16987695 original size:143 final size:141
Alignment explanation
Indices: 16987524--16987792 Score: 380
Period size: 143 Copynumber: 1.9 Consensus size: 141
16987514 TAAGGCCAAA
* * *
16987524 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGAGAGCTTTTTTCA-TCAATTTTACTGACAGTG
1 CAGGAACTACTGTAAAAAAAGAGCATCCACGTGAGAGCTTTTTTAAGT-AATTTTACTAACAGTG
* *
16987588 TATCCTGCTTGAAGCGTTTTTGACACCAT-TTGTTCAGAACCGTCTTCTCAAAATTATTTTTTCT
65 CATCATGCTTGAAGCGTTTTTGACACCATCTT-TTCAGAA-CGTCTTCTCAAAATTATTTTTTCT
16987652 CATAATTATTTTTT
128 CATAATTATTTTTT
* *
16987666 CAGGAACTACTGTAAAAAAAAGAGCATCCACGTGGGAGCTTTTTTAAGTAATTTTGCTAACAGTG
1 CAGGAACTACTGT-AAAAAAAGAGCATCCACGTGAGAGCTTTTTTAAGTAATTTTACTAACAGTG
* * * **
16987731 CATCATGTTTGAAGCGTTTTTTATATTATCTTTTCAGAACGTCTTCTCAAAATTATTTTTTC
65 CATCATGCTTGAAGCGTTTTTGACACCATCTTTTCAGAACGTCTTCTCAAAATTATTTTTTC
16987793 AGAAACTACT
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
142 36 0.32
143 73 0.65
144 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (141 bp):
CAGGAACTACTGTAAAAAAAGAGCATCCACGTGAGAGCTTTTTTAAGTAATTTTACTAACAGTGC
ATCATGCTTGAAGCGTTTTTGACACCATCTTTTCAGAACGTCTTCTCAAAATTATTTTTTCTCAT
AATTATTTTTT
Found at i:16987943 original size:34 final size:34
Alignment explanation
Indices: 16987865--16987991 Score: 111
Period size: 34 Copynumber: 3.8 Consensus size: 34
16987855 AAACACAAAA
* * *
16987865 TTATTTA--TAAAAAACTTAAACCATAATTTAAT
1 TTATTTATTTAAAAACCCTAAACCCTAATTTAAT
* * *
16987897 TAATTCT-CTTAAAAACCCTAATCCCTAATTTAAT
1 TTATT-TATTTAAAAACCCTAAACCCTAATTTAAT
* * *
16987931 TTATTTATTTAAAATCCCAAAAACCTAATTTAA-
1 TTATTTATTTAAAAACCCTAAACCCTAATTTAAT
*
16987964 TTA-ATATTTAAAAAACCCTAAACCCTAA
1 TTATTTATTT-AAAAACCCTAAACCCTAA
16987992 ACCTACCAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
32 9 0.12
33 20 0.27
34 46 0.61
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (34 bp):
TTATTTATTTAAAAACCCTAAACCCTAATTTAAT
Found at i:16987944 original size:68 final size:65
Alignment explanation
Indices: 16987865--16987991 Score: 141
Period size: 68 Copynumber: 1.9 Consensus size: 65
16987855 AAACACAAAA
** * *
16987865 TTATTTATAAAA-AACTTAAACCATAATTTAATTAAT-TCTCTTAAAAACCCTAATCCCTAATTT
1 TTATTTATAAAATAACAAAAACC-TAATTTAATTAATAT-T-TAAAAAACCCTAAACCCTAATTT
16987928 AAT
63 AAT
**
16987931 TTATTTATTTAAAATCCCAAAAACCTAATTTAATTAATATTTAAAAAACCCTAAACCCTAA
1 TTATTTA--TAAAATAACAAAAACCTAATTTAATTAATATTTAAAAAACCCTAAACCCTAA
16987992 ACCTACCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
66 7 0.14
67 18 0.35
68 19 0.37
69 7 0.14
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (65 bp):
TTATTTATAAAATAACAAAAACCTAATTTAATTAATATTTAAAAAACCCTAAACCCTAATTTAAT
Found at i:16990446 original size:2 final size:2
Alignment explanation
Indices: 16990441--16990491 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
16990431 ATATATAAAT
16990441 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
16990483 AA AG AG AG A
1 AG AG AG AG A
16990492 AATGGTATAG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16994406 original size:13 final size:13
Alignment explanation
Indices: 16994372--16994406 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
16994362 GTCATCATTT
16994372 ACCCATAACCAAA
1 ACCCATAACCAAA
16994385 ACCCTATAACCAAA
1 ACCC-ATAACCAAA
16994399 ACCCATAA
1 ACCCATAA
16994407 ACTCATACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.11
Consensus pattern (13 bp):
ACCCATAACCAAA
Found at i:16998072 original size:2 final size:2
Alignment explanation
Indices: 16998065--16998091 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16998055 TATTAAAATA
16998065 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
16998092 ATTGTGTGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16999905 original size:45 final size:44
Alignment explanation
Indices: 16999846--16999936 Score: 110
Period size: 45 Copynumber: 2.0 Consensus size: 44
16999836 TTTGGTTCGC
* * * *
16999846 TGTATTGGATTAGAGGTGTAATGGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGC-AATCAACTGTTTGGTTGAA
***
16999891 TGTAATGGAATAGAGGCGTAATAGCAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAATCAACTGTTTGGTTGAA
16999935 TG
1 TG
16999937 GAATAGAGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.29, C:0.07, G:0.30, T:0.35
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAATCAACTGTTTGGTTGAA
Found at i:17000122 original size:18 final size:17
Alignment explanation
Indices: 17000101--17000135 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17000091 TTATTATTAA
*
17000101 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
17000119 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
17000136 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:17000373 original size:14 final size:15
Alignment explanation
Indices: 17000318--17000375 Score: 57
Period size: 16 Copynumber: 3.9 Consensus size: 15
17000308 AAATAATTTA
* *
17000318 ATTATATTTAAACAT
1 ATTATAATTAAATAT
*
17000333 AATTATTATTAAATAT
1 -ATTATAATTAAATAT
17000349 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
17000363 A-TATAATTTAATA
1 ATTATAATTAAATA
17000376 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
13 9 0.25
14 4 0.11
15 11 0.31
16 12 0.33
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:17001660 original size:23 final size:23
Alignment explanation
Indices: 17001632--17001715 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
17001622 AACATAAACA
*
17001632 AATCAACACAATTTCCAGCAGAC
1 AATCAAAACAATTTCCAGCAGAC
*
17001655 AATCAAAACAATTTCCAGCAGCC
1 AATCAAAACAATTTCCAGCAGAC
* *
17001678 AATCATACCAATTTCCAGCAGAC
1 AATCAAAACAATTTCCAGCAGAC
17001701 AATCAAAACAATTTC
1 AATCAAAACAATTTC
17001716 AGAACAAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (23 bp):
AATCAAAACAATTTCCAGCAGAC
Found at i:17001743 original size:22 final size:21
Alignment explanation
Indices: 17001701--17001746 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
17001691 TCCAGCAGAC
* *
17001701 AATCAAAACAATTTCAGAACA
1 AATCAAAACAATATCAAAACA
*
17001722 AATCAAGACCAATATCAAAACA
1 AATCAA-AACAATATCAAAACA
17001744 AAT
1 AAT
17001747 GCAACAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.59, C:0.20, G:0.04, T:0.17
Consensus pattern (21 bp):
AATCAAAACAATATCAAAACA
Found at i:17002506 original size:10 final size:10
Alignment explanation
Indices: 17002491--17002518 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
17002481 AATTATATGC
17002491 TTTCTTATCG
1 TTTCTTATCG
17002501 TTTCTTATCG
1 TTTCTTATCG
17002511 TTTCTTAT
1 TTTCTTAT
17002519 AGATTAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.18, G:0.07, T:0.64
Consensus pattern (10 bp):
TTTCTTATCG
Found at i:17023560 original size:21 final size:21
Alignment explanation
Indices: 17023531--17023573 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
17023521 ATAATTATGC
17023531 AAAAAAATTA-AAAATATCAT
1 AAAAAAATTATAAAATATCAT
*
17023551 AAAAACAATTATCAAATATCAT
1 AAAAA-AATTATAAAATATCAT
17023573 A
1 A
17023574 TTTAATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 5 0.25
22 10 0.50
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAAAATTATAAAATATCAT
Done.